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PlantsP/PlantsT


NAR Molecular Biology Database Collection entry number 371
Tchieu, J.2, Fana, F.1, Fink, J.L.1, Harper, J.3, Nair, M.2, Niedner, R.H.1, Smith, D.W.2, Steube, K.1, Tam, T.1, Veretnik, S.1, Wang, D.1, Gribskov, M.1
1San Diego Supercomputer Center University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0537, USA
2Department of Biology University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0537, USA
3Department of Cell Biology The Scripps Research Institute 10550 N. Torrey Pines Road La Jolla, CA 92037, USA

Database Description

As one database with two functionally different web interfaces, PlantsP and PlantsT are plant-specific curated databases that combine sequence derived information with experimental functional genomics data. PlantsP focuses on proteins involved in the phosphorylation process (i.e. kinases and phosphatases), whereas PlantsT focuses on membrane transport proteins. Experimentally, PlantsP provides a resource for information on a collection of T-DNA insertion mutants (knockouts) in each kinase and phosphatase, primarily in Arabidopsis thaliana, and PlantsT uniquely combines experimental data regarding mineral composition (derived from inductively coupled plasma atomic emission spectroscopy) of mutant and wild-type strains. Both databases provide extensive information on motifs and domains, detailed information contributed by individual experts in their respective fields, and descriptive information drawn directly from the literature. PlantsP is available at http://plantsp.sdsc.edu and PlantsT is available at http://plantst.sdsc.edu.

Recent Developments

The original PlantsP database has been extended to include PlantsT as a second view based on a common data and software model. A proteotyp system for acquiring and peer-reviewing user annotation has been implemented and is in use with over 200 registered users.

Acknowledgements

This work is supported by the funding from National Science Foundation Plant Genome Program, DBI-9975808 (PlantsP) and DBI- 0077378 (PlantsT). This work is also assisted by the facilities of the National Biomedical Computation Resource at SDSC (NIH P41-RR08605).

References

1. Gribskov M, Fana F, Harper J, Hope DA, Harmon AC, Smith DW, Tax FE, Zhang G. (2001) PlantsP: a functional genomics database for plant phosphorylation. Nucleic Acids Res. Jan 1;29(1):111-3.
2. Van Belle D, Andre B. (2001) A genomic view of yeast membrane transporters. Curr Opin Cell Biol. Aug;13(4):389-98. Review.
3. Ward JM. (2001) Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana. Bioinformatics. Jun;17(6):560-3.
4. Krysan,P.J., Young,J.K. and Sussman,M.R. (1999). T-DNA as an Insertional Mutagen in Arabidopsis. Plant Cell, 2, 2283?2290.
5. Saier, M.H. (1999) A functional-phylogenetic system for the classification of transport proteins. J Cell Biochem.;Suppl 32-33:84-94. Review.
6. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. Sep 1;25(17):3389-402. Review.
7. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. Dec 15;25(24):4876-82.

Category: Plant databases

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